BN0341 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 2 2.8664e-05 7.9919e-03
Layer 3 1.1052e-04 2.0245e-02
Layer 1 1.7624e-01 3.4227e-01
WM 9.9994e-01 9.5896e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 2 1.8242 0.6734
SLC17A7 Layer 2 2.0039 0.5108
PRKAR1B Layer 2 2.0781 0.5004
CAMK2B Layer 2 1.9678 0.4985
GDI1 Layer 2 2.0723 0.4914
STMN1 Layer 2 1.9717 0.4900
TUBB Layer 3 1.9678 0.4862
TSC22D1 Layer 2 1.9014 0.4855
WAC Layer 2 1.8838 0.4832
PTPRN Layer 2 2.1055 0.4832
FXYD7 Layer 2 2.0918 0.4831
TSPYL1 Layer 2 1.9492 0.4793
THY1 Layer 2 2.1543 0.4787
PLD3 Layer 2 2.0547 0.4787
APBB1 Layer 3 2.0176 0.4785
ARPP19 Layer 2 1.9492 0.4752
STXBP1 Layer 2 2.0039 0.4728
GPI Layer 2 1.9854 0.4712
MAP1A Layer 2 1.9053 0.4710
GRIN1 Layer 2 2.0859 0.4703
PPP2R1A Layer 2 2.0352 0.4701
CNTN1 Layer 3 1.8545 0.4685
PREPL Layer 3 1.9209 0.4674
RANGAP1 Layer 2 1.9453 0.4657
GNAO1 Layer 2 2.0957 0.4656
IGSF8 Layer 2 1.8203 0.4614
KIF5C Layer 2 1.9053 0.4576
NDFIP1 Layer 2 1.9014 0.4573
PPP3CA Layer 2 1.8926 0.4552
DHCR24 Layer 2 1.8076 0.4544
EVL Layer 2 1.9541 0.4535
KLC1 Layer 2 2.0254 0.4533
NRGN Layer 2 1.8799 0.4524
SH3GL2 Layer 2 1.7910 0.4523
MEF2C Layer 2 2.0488 0.4522
OLFM1 Layer 2 1.9404 0.4517
RPL11 Layer 2 1.8184 0.4515
TLN2 Layer 2 1.9014 0.4515
LY6H Layer 2 2.2363 0.4509
MEG3 Layer 2 2.0723 0.4509
NUCKS1 Layer 2 1.9316 0.4508
PTMS Layer 2 1.9902 0.4504
DNAJB2 Layer 2 1.8037 0.4503
CTSD Layer 2 1.9473 0.4500
RAB3A Layer 2 2.0176 0.4496
GNAQ Layer 2 1.8330 0.4487
CHN1 Layer 2 1.9053 0.4487
YWHAB Layer 2 2.0176 0.4485
STMN3 Layer 2 1.9541 0.4483
MAPK3 Layer 2 1.9229 0.4478

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0341
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0341_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0341/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0341/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0341/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0341/report/PD/BN0341_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0341/report/PD/BN0341_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-10 23:47:39
  • Number of Processes: 10
  • Spending Time: 0h 2m